<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div>Dear gate users,</div><div><br data-mce-bogus="1"></div><div>I found the solution to my problem! It was very silly, but I'm not a physicist and I'm still discovering GATE.</div><div>- the simulation volume was way to big compared to the volume of the dose distribution I wanted to see. With few particles, I don't think any particles deposited a dose in the volume.</div><div>- I lowered the energy of the source from 10 MeV to 30 keV.</div><div>- I increased the number of primaries.</div><div><br data-mce-bogus="1"></div><div>Kind regards,<br data-mce-bogus="1"></div><div>Sarah Blind</div><div><br data-mce-bogus="1"></div><div><br></div><div><span id="zwchr" data-marker="__DIVIDER__">----- Le 14 Déc 21, à 13:05, Sarah Blind <sarah.blind@univ-lorraine.fr> a écrit :<br></span></div><div data-marker="__QUOTED_TEXT__"><blockquote style="border-left:2px solid #1010FF;margin-left:5px;padding-left:5px;color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;"><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div>Dear gate users,<br></div><br><div>I'm still stuck on the same problem (the output has only 0 values) and I'm wondering if it could be linked with a problem of dose calculation algorithm? </div><div>Does someone understand the following sentence in 8.2.3.2 in <a href="http://www.opengatecollaboration.org/" target="_blank">http://www.opengatecollaboration.org/</a><br><br></div><blockquote><div>If the size of the image voxel is smaller than the size of the dosel of the DoseActor it can lead to undesired results. <br></div></blockquote><br><div>I'm ok with the <em>dosel of the DoseActor</em>, but what does <em>image voxel</em> here exaclty mean?<br></div><br><div>I will also look at matplotlib for analysing my code, but still it does not explain why the visualization with Gate works but the output files opened with ImageJ have only 0 values...<br></div><br><div>If someone has an idea what could be the problem, thank you very much for your help!<br></div><br><div>Sarah Blind<br></div><br><br><div><span id="zwchr">----- Le 13 Déc 21, à 16:29, Musajoya Joya <musajoyajoya@gmail.com> a écrit :<br></span></div><div><blockquote style="border-left:2px solid #1010FF;margin-left:5px;padding-left:5px;color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;"><div dir="ltr"><div dir="ltr"><div class="gmail_default" style="font-family:times new roman,serif;font-size:large;color:#000000">Dear friends, </div><div class="gmail_default" style="font-family:times new roman,serif;font-size:large;color:#000000"><br></div><div class="gmail_default" style="font-family:"times new roman",serif;font-size:large"><span style="color:rgb(0,0,0)">I have the same problem. I am trying to do dynamic intensity-modulated brachytherapy. The movement and the radiation emission visualization look ok but the actors do not record any dose even with 200 million particles. I use the output format of .mhd and or .txt, but for both the dose is zero. what would be the reason(s)? Doseactors score the dose even when </span><font color="#9900ff">/gate/application/noGlobalOutput</font><font color="#000000"> is active in static mode. </font></div><div class="gmail_default" style="font-family:times new roman,serif;font-size:large;color:#000000">Please any GATE expert has a look at my code and point out the problem. </div><div class="gmail_default" style="font-family:times new roman,serif;font-size:large;color:#000000">PLEASE HELP!!</div><div class="gmail_default" style="font-family:times new roman,serif;font-size:large;color:#000000">#=====================================================<br># PHYSICS<br>#=====================================================<br>/gate/physics/addPhysicsList emstandard_opt3<br>/gate/physics/Gamma/SetCutInRegion world 10 mm<br>/gate/physics/Electron/SetCutInRegion world 10 mm<br>/gate/physics/Positron/SetCutInRegion world 10 mm<br>#/gate/physics/Gamma/SetCutInRegion sc4 0.1 mm<br>#/gate/physics/Electron/SetCutInRegion sc4 1 m<br>/gate/physics/displayCuts<br>#=====================================================<br># DETECTORS<br>#=====================================================<br>### Target ##############<br>/gate/actor/addActor DoseActor targetdose<br>/gate/actor/targetdose/attachTo vaginatarget <br>/gate/actor/targetdose/stepHitType random<br>/gate/actor/targetdose/setVoxelSize 2 2 2 mm<br>/gate/actor/targetdose/save output/target/targetdose.txt<br>/gate/actor/targetdose/saveEveryNSeconds 60<br>/gate/actor/targetdose/enableDose true<br>/gate/actor/targetdose/enableUncertaintyDose true<br>/gate/actor/targetdose/enableSquaredDose true<br><br># filter<br>/gate/actor/targetdose/addFilter energyFilter<br>/gate/actor/targetdose/energyFilter/setEmin 0.01 MeV<br>/gate/actor/targetdose/energyFilter/setEmax 2.5 MeV<br>#=====================================================<br>#rotation<br>#=====================================================<br>/gate/outerlayer/moves/insert rotation<br>/gate/outerlayer/rotation/setSpeed 1 deg/s<br>/gate/outerlayer/rotation/setAxis 0 0 -1<br>/gate/outerlayer/placement/setRotationAngle 90 deg<br><br>/gate/application/setTimeSlice 1. s<br>/gate/application/setTimeStart 0. s<br>/gate/application/setTimeStop 90. s<br>#/gate/application/startDAQ<br>#=====================================================<br># INITIALISATION<br>#=====================================================<br>/gate/run/initialize<br>#=====================================================<br># BEAMS<br>#=====================================================<br>#Description of co-60 source<br>/gate/source/addSource co60s gps<br>/gate/source/co60s/gps/particle gamma<br>/gate/source/co60s/gps/energytype UserSpectrum<br>/gate/source/co60s/gps/setSpectrumFile data/co60spectrum.txt<br>/gate/source/co60s/gps/hist/type energy<br>/gate/source/co60s/attachTo sourceSeed<br>/gate/source/co60s/gps/type Volume<br>/gate/source/co60s/gps/shape Cylinder<br>/gate/source/co60s/gps/radius 0.025 cm<br>/gate/source/co60s/gps/halfz 0.175 cm<br>#/gate/source/co60s/gps/centre 0.85 0.0 11 cm<br>/gate/source/co60s/gps/ang/type iso<br>/gate/source/co60s/visualize 10000 red 5<br>/gate/source/list<br>#=====================================================<br># START BEAMS<br>#=====================================================<br>/gate/random/setEngineName MersenneTwister<br>/gate/random/setEngineSeed auto</div><div class="gmail_default" style="font-family:times new roman,serif;font-size:large;color:#000000">/gate/application/setTotalNumberOfPrimaries 10000000<br>/gate/application/start<br></div><div class="gmail_default" style="font-family:times new roman,serif;font-size:large;color:#000000"><br></div><div><div dir="ltr"><div dir="ltr"><p style="color:rgb(0,0,0)"><i><font face="comic sans ms, sans-serif">Kind Regards</font></i></p><p style="color:rgb(0,0,0)"><em><font face="comic sans ms, sans-serif">Musa Joya</font></em></p><p style="color:rgb(0,0,0)"><em><font face="comic sans ms, sans-serif">Ph.D. candidate in Medical Physics </font></em></p><p style="color:rgb(0,0,0)"><em><font face="comic sans ms, sans-serif">Tehran University of Medical Sciences</font></em></p><p style="color:rgb(0,0,0)"><em><font face="comic sans ms, sans-serif">Tehran, Iran &</font></em></p><p style="color:rgb(0,0,0)"><em><font face="comic sans ms, sans-serif">Lecturer of Medical Physics </font></em></p><p style="color:rgb(0,0,0)"><em><font face="comic sans ms, sans-serif">Kabul University of Medical Sciences</font></em></p><p style="color:rgb(0,0,0)"><em><font face="comic sans ms, sans-serif">Kabul, Afghanistan</font></em></p><p style="color:rgb(0,0,0)"><em><font face="comic sans ms, sans-serif">Mobile and Telegram & WhatsApp: +989381560693</font></em></p></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 13 Dec 2021 at 17:43, Sarah Blind <<a href="mailto:sarah.blind@univ-lorraine.fr" target="_blank">sarah.blind@univ-lorraine.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div style="font-family:arial,helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><div>Yes !</div><br><div><span id="m_6613091206310161751gmail-m_-6403290513620715616gmail-m_-8142501224507543530zwchr">----- Le 13 Déc 21, à 14:40, Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> a écrit :<br></span></div><div><blockquote style="border-left:2px solid rgb(16,16,255);margin-left:5px;padding-left:5px;color:rgb(0,0,0);font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt">
Did you increase your number of primaries from 1?<br>
<br>
<div dir="ltr">Matthew</div>
<div dir="ltr"><br>
<blockquote>On Dec 13, 2021, at 9:00 AM, Sarah Blind <<a href="mailto:sarah.blind@univ-lorraine.fr" target="_blank">sarah.blind@univ-lorraine.fr</a>> wrote:<br>
<br>
</blockquote>
</div>
<blockquote>
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<span style="font-weight:bold;font-size:12px">CAUTION:</span> The Sender of this email is not from within Dalhousie.</div>
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<div style="font-family:arial,helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<div>I still have the same problem even without <span style="color:rgb(0,0,0);font-family:Helvetica,Arial,sans-serif;font-size:16px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">
<span> </span>/gate/application/noGlobalOutput ...</span></div>
<div><br>
</div>
<div><span id="m_6613091206310161751gmail-m_-6403290513620715616gmail-m_-8142501224507543530zwchr">----- Le 13 Déc 21, à 13:43, Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> a écrit :<br>
</span></div>
<div>
<blockquote style="border-left:2px solid rgb(16,16,255);margin-left:5px;padding-left:5px;color:rgb(0,0,0);font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt">
Hi Sarah,
<div><br>
</div>
<div>You have the output disabled. Remove /gate/application/noGlobalOutput from your macro and try again.<br>
<br>
Best,<br>
<div dir="ltr">Matthew</div>
<div dir="ltr"><br>
<blockquote>On Dec 13, 2021, at 6:19 AM, Sarah Blind <<a href="mailto:sarah.blind@univ-lorraine.fr" target="_blank">sarah.blind@univ-lorraine.fr</a>> wrote:<br>
<br>
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<span style="font-weight:bold;font-size:12px">CAUTION:</span> The Sender of this email is not from within Dalhousie.</div>
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<div>Dear Gate users,</div>
<div><br>
</div>
<div>I am trying to follow the exercices (1 and 2) of <a href="https://davidsarrut.pages.in2p3.fr/gate-exercices-site/docs/welcome/" target="_blank">
https://davidsarrut.pages.in2p3.fr/gate-exercices-site/docs/welcome/</a>.<br>
</div>
<div>When I open the output files (with ImageJ) I obtain only 0 values. <br>
</div>
<div>Does anyone have any idea why those dose distribution values are all zero?<br>
</div>
<blockquote>
<div><br>
<br>
# Visualization<br>
/vis/open OGLIQt<br>
/vis/drawVolume<br>
/vis/viewer/flush<br>
/tracking/storeTrajectory 1<br>
/vis/scene/add/trajectories<br>
/vis/scene/endOfEventAction accumulate<br>
/vis/modeling/trajectories/create/drawByParticleID<br>
<br>
/gate/geometry/setMaterialDatabase ../data/GateMaterials.db<br>
<br>
# World<br>
/gate/world/geometry/setXLength 1 m<br>
/gate/world/geometry/setYLength 1 m<br>
/gate/world/geometry/setZLength 1 m<br>
/gate/world/setMaterial Air<br>
<br>
# Water Box<br>
/gate/world/daughters/name waterbox<br>
/gate/world/daughters/insert box<br>
/gate/waterbox/geometry/setXLength 40 cm<br>
/gate/waterbox/geometry/setYLength 40 cm<br>
/gate/waterbox/geometry/setZLength 40 cm<br>
/gate/waterbox/placement/setTranslation 0 0 25 cm<br>
/gate/waterbox/setMaterial Water<br>
/gate/waterbox/vis/setVisible 1<br>
/gate/waterbox/vis/setColor blue<br>
<br>
# aluminium box<br>
/gate/world/daughters/name alubox<br>
/gate/world/daughters/insert box<br>
/gate/alubox/geometry/setXLength 5 cm<br>
/gate/alubox/geometry/setYLength 5 cm<br>
/gate/alubox/geometry/setZLength 5 cm<br>
/gate/alubox/placement/setTranslation 0 0 15 cm<br>
/gate/alubox/setMaterial Aluminium<br>
/gate/alubox/vis/setVisible 1<br>
/gate/alubox/vis/setColor yellow<br>
<br>
#=========<br>
# PHYSICS<br>
#=========<br>
<br>
/gate/physics/addPhysicsList emstandard_opt3<br>
<br>
/gate/physics/Gamma/SetCutInRegion world 10 mm<br>
/gate/physics/Electron/SetCutInRegion world 10 mm<br>
/gate/physics/Positron/SetCutInRegion world 10 mm<br>
<br>
/gate/physics/Gamma/SetCutInRegion waterbox 0.01 mm<br>
/gate/physics/Electron/SetCutInRegion waterbox 0.01 mm<br>
/gate/physics/Positron/SetCutInRegion waterbox 0.01 mm<br>
<br>
/gate/physics/displayCuts<br>
<br>
<br>
#===========<br>
# DETECTORS<br>
#===========<br>
<br>
/gate/actor/addActor DoseActor depthdose<br>
/gate/actor/depthdose/save output/gamma-depth.txt<br>
/gate/actor/depthdose/attachTo waterbox<br>
/gate/actor/depthdose/stepHitType random<br>
/gate/actor/depthdose/setPosition 0 0 0 cm<br>
/gate/actor/depthdose/setResolution 1 1 100<br>
/gate/actor/depthdose/saveEveryNSeconds 60<br>
/gate/actor/depthdose/enableEdep true<br>
/gate/actor/depthdose/enableUncertaintyEdep true<br>
/gate/actor/depthdose/enableDose true<br>
/gate/actor/depthdose/enableUncertaintyDose true<br>
/gate/actor/depthdose/enableNumberOfHits true<br>
<br>
/gate/actor/addActor DoseActor doseprofile<br>
/gate/actor/doseprofile/save output/gamma-profile.txt<br>
/gate/actor/doseprofile/attachTo waterbox<br>
/gate/actor/doseprofile/stepHitType random<br>
/gate/actor/doseprofile/setPosition 0 0 4 cm<br>
/gate/actor/doseprofile/setResolution 100 1 1<br>
/gate/actor/doseprofile/setSize 5 40 40 cm<br>
/gate/actor/doseprofile/saveEveryNSeconds 60<br>
/gate/actor/doseprofile/enableEdep true<br>
/gate/actor/doseprofile/enableUncertaintyEdep true<br>
/gate/actor/doseprofile/enableDose true<br>
/gate/actor/doseprofile/enableUncertaintyDose true<br>
/gate/actor/doseprofile/enableNumberOfHits true<br>
<br>
/gate/actor/addActor SimulationStatisticActor stat<br>
/gate/actor/stat/save output/gamma-stat.txt<br>
/gate/actor/stat/saveEveryNSeconds 60<br>
<br>
/gate/actor/addActor DoseActor doseDistribution3D_1<br>
/gate/actor/doseDistribution3D_1/save output/doseDistribution3D_1.hdr<br>
/gate/actor/doseDistribution3D_1/attachTo waterbox<br>
/gate/actor/doseDistribution3D_1/stepHitType random<br>
/gate/actor/doseDistribution3D_1/setPosition 0.0 0.0 0.0 um<br>
/gate/actor/doseDistribution3D_1/setSize 40.0 40.0 40.0 um<br>
/gate/actor/doseDistribution3D_1/setResolution 200 200 200<br>
/gate/actor/doseDistribution3D_1/enableDose true<br>
/gate/actor/doseDistribution3D_1/saveEveryNSeconds 60<br>
<br>
<br>
#=============<br>
# INITIALISATION<br>
#==============<br>
<br>
/gate/run/initialize<br>
<br>
#================<br>
# BEAMS / SOURCE<br>
#================<br>
<br>
/gate/source/addSource mybeam gps<br>
/gate/source/mybeam/gps/particle gamma<br>
/gate/source/mybeam/gps/pos/type Beam<br>
/gate/source/mybeam/gps/pos/rot1 1 1 1<br>
#/gate/source/mybeam/gps/pos/rot2 0 0 0<br>
/gate/source/mybeam/gps/pos/shape Circle<br>
/gate/source/mybeam/gps/pos/centre 0 0 0 mm<br>
/gate/source/mybeam/gps/pos/sigma_x 3 mm<br>
/gate/source/mybeam/gps/pos/sigma_y 3 mm<br>
/gate/source/mybeam/gps/ene/mono 10 MeV<br>
/gate/source/mybeam/gps/ene/type Gauss<br>
/gate/source/mybeam/gps/ene/sigma 1.0 MeV<br>
/gate/source/mybeam/gps/direction 0 0 1<br>
<br>
<br>
#=============<br>
# START BEAMS<br>
#=============</div>
<div><br>
/gate/random/setEngineName MersenneTwister<br>
/gate/random/setEngineSeed auto<br>
<br>
/gate/application/noGlobalOutput<br>
/gate/application/setTotalNumberOfPrimaries 1<br>
/gate/application/start<br>
<br>
<br>
</div>
</blockquote>
<div><br>
</div>
<div>Many thanks for your help,<br>
</div>
<div><br>
</div>
<div>Sarah Blind<br>
</div>
</div>
</div>
<span>_______________________________________________</span><br>
<span>Gate-users mailing list</span><br>
<span><a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a></span><br>
<span><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></span><br></div>
</blockquote>
</div>
<br>
</blockquote>
</div>
<div><br>
</div>
<div>-- <br>
</div>
<div>Sarah Blind<br>
Ingénieure de recherche - CNRS<br>
Centre de Recherche en Automatique de Nancy (CRAN) <br>
Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences (BioSiS)<br>
Site de la faculté de médecine <br>
9, Avenue de la Forêt de Haye <br>
54505 Vandoeuvre les Nancy <br>
Tél : 03.72.74.61.13</div>
</div>
</div>
</div>
</blockquote><br></blockquote></div><br><div>-- <br></div><div>Sarah Blind<br>Ingénieure de recherche - CNRS<br>Centre de Recherche en Automatique de Nancy (CRAN) <br>Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences (BioSiS)<br>Site de la faculté de médecine <br>9, Avenue de la Forêt de Haye <br>54505 Vandoeuvre les Nancy <br>Tél : 03.72.74.61.13</div></div></div>_______________________________________________<br>
Gate-users mailing list<br>
<a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br>
<a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" rel="noreferrer" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br></blockquote></div>
</div><br></blockquote></div><br><div>-- <br></div><div>Sarah Blind<br>Ingénieure de recherche - CNRS<br>Centre de Recherche en Automatique de Nancy (CRAN) <br>Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences (BioSiS)<br>Site de la faculté de médecine <br>9, Avenue de la Forêt de Haye <br>54505 Vandoeuvre les Nancy <br>Tél : 03.72.74.61.13</div></div><br></blockquote></div><div><br></div><div data-marker="__SIG_POST__">-- <br></div><div>Sarah Blind<br>Ingénieure de recherche - CNRS<br>Centre de Recherche en Automatique de Nancy (CRAN) <br>Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences (BioSiS)<br>Site de la faculté de médecine <br>9, Avenue de la Forêt de Haye <br>54505 Vandoeuvre les Nancy <br>Tél : 03.72.74.61.13</div></div></body></html>